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Simon Lin
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270
@simon-lin-1272
Last seen 10.2 years ago
Hello,
I loaded a few CEL file from MOE430A experiments. Strangely, many PM
values are negative! As a result, RMA and other routines did not work.
Any ideas?? See scripts below. I am puzzled!
I am running Bioconductor 1.6, R 2.1.0, with moe430acdf loaded.
Thanks!
Simon
################################################################
> result.batch<- ReadAffy(filenames=CEL.fileNames)
> result.batch
AffyBatch object
size of arrays=712x712 features (11886 kb)
cdf=MOE430A (22690 affyids)
number of samples=3
number of genes=22690
annotation=moe430a
>
> x<-pm (result.batch)
> dim (x)
[1] 249958 3
> x[1:10,]
P3-real.CEL P4-real.CEL P5-real.CEL
[1,] 1.001874e-23 -2.117582e-22 4.567573e-08
[2,] 1.603000e+03 1.240000e+03 2.319708e-39
[3,] -8.589935e+09 1.454000e+02 2.759000e+03
[4,] 3.503246e-44 8.100000e+01 4.539706e-08
[5,] 5.238000e+02 4.010000e+02 2.319436e-39
> result.degradation<- AffyRNAdeg(result.batch)
Error in var(x, na.rm = na.rm) : missing observations in cov/cor
In addition: There were 50 or more warnings (use warnings() to see the
first 50)
>
> MAplot (result.batch)
Error in rowQ(imat, half) : cannot handle missing values -- yet
In addition: Warning message:
NaNs produced in: log(x, base)